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Add exonerate test files
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25
Tests/Exonerate/README.txt
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25
Tests/Exonerate/README.txt
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EXONERATE TEST DATA FILES
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=========================
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This directory contains various data files for testing the
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Exonerate-related code in Biopython. All files are grouped by
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Exonerate release version, from the most recent first.
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Exonerate 2.2
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-------------
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exn_22_m_affine_local.exn affine:local model alignment
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exn_22_m_cdna2genome.exn cdna2genome model alignment
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exn_22_m_coding2coding.exn coding2coding model alignment
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exn_22_m_coding2genome.exn coding2genome model alignment
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exn_22_m_est2genome.exn est2genome model alignment
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exn_22_m_genome2genome.exn genome2genome model alignment
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exn_22_m_ner.exn ner model alignment
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exn_22_m_protein2dna.exn protein2dna model alignment
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exn_22_m_protein2genome.exn protein2genome model alignment
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exn_22_m_ungapped.exn ungapped model alignment (default)
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exn_22_m_ungapped_trans.exn ungapped:translated model alignment
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exn_22_o_vulgar_cigar.exn genome2genome alignment with vulgar and cigar lines only
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exn_22_o_vulgar.exn genome2genome alignment with vulgar lines only
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193
Tests/Exonerate/exn_22_m_affine_local.exn
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193
Tests/Exonerate/exn_22_m_affine_local.exn
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Command line: [exonerate -m affine:local ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
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Hostname: [blackbriar]
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C4 Alignment:
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------------
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Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
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Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
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Model: affine:local:dna2dna
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Raw score: 6150
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Query range: 0 -> 1230
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Target range: 1319275 -> 1318045
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1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 56
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319220
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57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
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1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
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113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 168
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1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108
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169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 224
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052
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225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
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281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 336
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940
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337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 392
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884
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393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
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1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
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449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 504
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772
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505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 560
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716
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561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
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617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 672
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604
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673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 728
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548
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729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
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1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
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785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 840
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436
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841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 896
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1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380
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897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
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953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1008
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268
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1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1064
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212
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1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
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1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1176
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100
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1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
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1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
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C4 Alignment:
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------------
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Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
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Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
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Model: affine:local:dna2dna
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Raw score: 359
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Query range: 83 -> 552
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Target range: 253990 -> 254474
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84 : ACCTAAGAGGAAGGTGGGCAGACCAGGCAGAAAA-AGGATT--GACTCTGAAGCTAAG : 138
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||| |||| ||||| ||| | | ||| ||| | |||| || ||||| |||||
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253991 : ACCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAG : 254048
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139 : AGTAGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGAGATAGGAAAGAAG : 196
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254049 : CAGAAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGA : 254106
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197 : CCAAAATGAAGAGTTTGCAAGAGAGGGT--AGAGTTACTAGAACAGAAAGATGC-GCA : 251
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|| |||||| ||| | ||| ||| | |||| ||| | || | || |||
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254107 : GGAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTT--TAG-AGAGTATTCAGCAGCA : 254161
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252 : GAATAAGACTACCACGGACTTTTTACTATGTTC-TTTAAAAAGTTTACTGTCGGAAAT : 308
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||| | | | | ||||||| | | |||| | | | || || |
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254162 : AAATGA-AGTGGAAGCTACTTTTTTGAGGGACCAGTTAATCACTCTGGTGAATGAGTT : 254218
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309 : TACAAAATAT-----AGAGCTAAGAATT--CTGATGA-TGAAAGAATA-TTAGCCTTC : 357
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254219 : AAAAAAATATAGACCAGAGACAAGAAATGACTCAAAAGTGCTGGAATATTTAGCAAGG : 254276
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358 : CTCGA---TGATCTGCA-AGAACAACAGAAAAGGGAAA--AC-GAAAAAG-GA-ACAA : 406
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| || | || |||| ||| | | || | || || | || || || |||
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254277 : CGAGATCCTAATTTGCATTTTTCAAAAAATAACGTTAACCACAGCAATAGCGAGCCAA : 254334
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407 : GT-ACAGCAGTTAGCAAGGCTG-CA---AAGGAATTGCCATCGCCTAATTCAGATGAA : 459
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254335 : TTGACA-CA---CCCAATGATGACATACAAGAAAATG--TTAAACAAA---AGATGAA : 254383
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460 : -AACATGACTGTGAACA-CAAGTATAGAAGTACAGCCGCACACTCAAGAGAATGAGAA : 515
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|| | | | || | | | | || ||| | || ||| || | | ||
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254384 : TTTCACG--TTTCAATATCCGCTTGATAACGACAACGACAACGACAACAG--TAAAAA : 254437
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516 : AGTTATGTGGAACA--TAGGCTCATGGAACGCTCCCAGT : 552
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|| | | |||| || ||| || | ||| |||
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254438 : TGT--GGGGAAACAATTACCTTCACCAAATGATCCAAGT : 254474
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C4 Alignment:
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------------
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Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
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Target: gi|330443715|ref|NC_001146.8| Saccharomyces cerevisiae S288c chromosome XIV, complete sequence
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Model: affine:local:dna2dna
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Raw score: 219
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Query range: 60 -> 517
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Target range: 454073 -> 454531
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61 : ATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTG-GGCAGACCAGGCAGAAAA : 117
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454074 : ATGATGATATATTA-GATGGGG-ATG-AAGATGAGCCAGAGGAAGAGGATGAAAATGA : 454128
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118 : AGGAT-TGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGA--ATAGGG-CAGCTCA- : 171
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454129 : AGGCGATGACGAAGAAGATACT--TATGACAGCGGTCTTGATGAAACTGACCGTTTAG : 454184
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172 : ACGAGCGTTCCGAGATAGGAA-AGA-AGCCAAAATGAAGA-GTTTGCAAGA-GAGGGT : 224
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| || || | || || | ||| ||||| | ||| | || ||| ||
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454185 : AAGAAGGT-CGGAAATTGATTCAGATAGCCATTACAAAGTTGCTTCAAAGTCGAATAA : 454241
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225 : AGAGTTACTAGAAC-AGAAAGATGCGCAGAATAA--GACTACCACGGACTTTTTACTA : 279
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454242 : TGGCTTCTTATCATGAGAAACAGGCAGATAATAACAGACTAAAAC-----TTCTACAA : 454294
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280 : TGTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGATG : 337
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454295 : -GAACTAGAAGAAGAAAAAAGAAAGAAAAGAGAGAAGGAAGA---AAAAAAGCAGAAA : 454348
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338 : ATGAAAGAATATTAGCCTTCCTCGATGAT-CTGCAAGA---A-CAACAGAAAAGGGAA : 390
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454349 : AAAAGAGAAAAAGAGAAAGAAAAGAAGAGGCTGCAACAGTTAGCTAAAGAGGAAGAAA : 454406
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391 : AACGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCA-AAGGAATTGCCATCGCCT : 447
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||||||||||| ||| | || | || |||||| | |||||||| | || |
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454407 : AACGAAAAAGG--GAAGAAGAGAA---AGAAAGGCTAAAGAAGGAATTAGAAGAGCGT : 454459
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448 : -AATTCAGATGAAAACATG-ACTGTGAACACAAG-TATAGAAGTACAGCCGCACACTC : 502
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|| | ||| || | | | | | | | | | | ||||| | | | | |
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454460 : GAAATGAGAAGACGAGAGGCTCAAAGGAAAAAGGTTGAAGAAGCCAAACGGAAGAAAG : 454517
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503 : AAGAGAATGAGAAAG : 517
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| ||| | |||||||
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454518 : ACGAGGA-GAGAAAG : 454531
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-- completed exonerate analysis
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267
Tests/Exonerate/exn_22_m_cdna2genome.exn
Normal file
267
Tests/Exonerate/exn_22_m_cdna2genome.exn
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@ -0,0 +1,267 @@
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Command line: [exonerate -m cdna2genome ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
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Hostname: [blackbriar]
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C4 Alignment:
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------------
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Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
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Model: cdna2genome
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Raw score: 6146
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Query range: 0 -> 1230
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Target range: 1319275 -> 1318045
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1 : TGG : 56
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ATrpGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ATrpGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA
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1319275 : TGG : 1319220
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||||
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57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108
|
||||
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169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
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1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052
|
||||
|
||||
225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
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||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940
|
||||
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||||
337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 392
|
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884
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||||
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393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 504
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772
|
||||
|
||||
505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 560
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716
|
||||
|
||||
561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 672
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604
|
||||
|
||||
673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 728
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548
|
||||
|
||||
729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 840
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436
|
||||
|
||||
841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 896
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380
|
||||
|
||||
897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1008
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268
|
||||
|
||||
1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1064
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212
|
||||
|
||||
1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1176
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100
|
||||
|
||||
1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: cdna2genome
|
||||
Raw score: 6146
|
||||
Query range: 1230 -> 0
|
||||
Target range: 1318045 -> 1319275
|
||||
|
||||
1230 : CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTT : 1175
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318046 : CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTT : 1318101
|
||||
|
||||
1174 : TGCAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATG : 1119
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318102 : TGCAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATG : 1318157
|
||||
|
||||
1118 : TGG : 1063
|
||||
TCCAACGATGAATATTTTrpTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
TCCAACGATGAATATTTTrpTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGA
|
||||
1318158 : TGG : 1318213
|
||||
|
||||
1062 : CGCTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTC : 1007
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318214 : CGCTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTC : 1318269
|
||||
|
||||
1006 : GAATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGA : 951
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318270 : GAATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGA : 1318325
|
||||
|
||||
950 : TTCAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTT : 895
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318326 : TTCAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTT : 1318381
|
||||
|
||||
894 : GGTCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGG : 839
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318382 : GGTCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGG : 1318437
|
||||
|
||||
838 : GAAGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGG : 783
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318438 : GAAGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGG : 1318493
|
||||
|
||||
782 : TCAATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGA : 727
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318494 : TCAATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGA : 1318549
|
||||
|
||||
726 : GTGCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTC : 671
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318550 : GTGCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTC : 1318605
|
||||
|
||||
670 : TATCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTT : 615
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318606 : TATCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTT : 1318661
|
||||
|
||||
614 : TCGTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATT : 559
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318662 : TCGTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATT : 1318717
|
||||
|
||||
558 : GGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTT : 503
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318718 : GGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTT : 1318773
|
||||
|
||||
502 : GAGTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTA : 447
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318774 : GAGTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTA : 1318829
|
||||
|
||||
446 : GGCGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTT : 391
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318830 : GGCGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTT : 1318885
|
||||
|
||||
390 : TTCCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCAT : 335
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318886 : TTCCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCAT : 1318941
|
||||
|
||||
334 : CAGAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACAT : 279
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318942 : CAGAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACAT : 1318997
|
||||
|
||||
278 : AGTAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTAC : 223
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318998 : AGTAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTAC : 1319053
|
||||
|
||||
222 : CCTCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAG : 167
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319054 : CCTCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAG : 1319109
|
||||
|
||||
166 : CTGCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTG : 111
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319110 : CTGCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTG : 1319165
|
||||
|
||||
110 : CCTGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTT : 55
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319166 : CCTGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTT : 1319221
|
||||
|
||||
54 : CTTCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT : 1
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319222 : CTTCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT : 1319275
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: cdna2genome
|
||||
Raw score: 518
|
||||
Query range: 0 -> 516
|
||||
Target range: 85010 -> 667216
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAAGC : 58
|
||||
|||| || | |||| | |||||| |||| | | | |||| ||||||||||
|
||||
85011 : ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAACAGG----ATGAAGAAGC : 85059
|
||||
|
||||
59 : AAATGTT >>>> Target Intron 1 >>>> GCTA-AATAAAGATGGAACACC : 86
|
||||
||| | |++ 168908 bp -+|| | ||| || | | |||
|
||||
85060 : AAAAGATgt.........................tgGCGAGGATAGCGA--GCA-ACC : 253993
|
||||
|
||||
87 : TAAGAGGAAGGTGGGCAGACCAGGCAGAAA--AAGGATT-GACTCTGAAGCTAAGAGT : 141
|
||||
|||| ||||| ||| | | ||| ||| ||| || || ||||| |||||
|
||||
253994 : GAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAGCAG : 254051
|
||||
|
||||
142 : AGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGAGATAGGAAAGAAGCCA : 199
|
||||
| |||||||||||| ||| |||| |||||| |||| || | || | || || |
|
||||
254052 : AAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGAGGA : 254109
|
||||
|
||||
200 : AAATGAAGAGTTTGCAAGAGAGGGTA >>>> Target Intron 2 >>>> GAG : 228
|
||||
| |||||| ||| | ||| ||||-- 96824 bp -+| |
|
||||
254110 : AGATGAAGGAATTGGAGAAGAAGGTAca.........................tgGGG : 350962
|
||||
|
||||
229 : TTACTAGAACA--GAAAGATGCGCAGAATA--AGACTACCACGGACTT-TTTACTATG : 281
|
||||
| | || | || |||| | ||||| || ||||| ||| ||| |||
|
||||
350963 : TGATTATATCATTTCTGGATGAG--GAATACCTGAAGACCAC--TCTTCATTAAAATG : 351016
|
||||
|
||||
282 : TTCTTTAAAAAGTTTACTGTCGGAAAT-TACAAAATATAG >>>> Target Intr : 321
|
||||
||||||||||| | | || | ||| || | | | |||-+ 122118 b
|
||||
351017 : TTCTTTAAAAA-TATTCTTTTGGATATATTCTA---CTAGtt................ : 351055
|
||||
|
||||
322 : on 3 >>>> AGCTAAGAATTCTGATGATG-----AAAGAA >>>> Target In : 347
|
||||
p ++| |||||||||||| ||| ||||||-+ 193839
|
||||
351056 : .........agATGGAAGAATTCTGATAATGCTGTAAAAGAAat.............. : 473204
|
||||
|
||||
348 : AG : 385
|
||||
tron 4 >>>> TATTAGCCTTCC--TCGATGATCTGCA--A-GAACAACAGAAAAr
|
||||
bp ++| |||| || | ||||| | || || | ||| | | ||
|
||||
...........agTCATAGCGTTACGTTCGAT-ACCTTCACTACGAAGATCCAAACSe
|
||||
473205 : TC : 667083
|
||||
|
||||
386 : GGAAAACGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCG : 442
|
||||
gGluAsnGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSer
|
||||
:::......! ! ! .!. ! ... !:!:... +|+||+:!:
|
||||
rPheSerSerSerAspLysPheLeuThrPhePheSerLeuSerSerPheLeuProThr
|
||||
667084 : TTTTTCTAGTTCCGATAAATTCCTTACCTTCTTTTCACTTTCCTCTTTTCTCCCTACA : 667140
|
||||
|
||||
443 : CCTAATTCAGATGAA : 499
|
||||
ProAsnSerAspGluAACATGACTGT-GA-ACA-CAAGTATAGAAGTACAGCCGCACA
|
||||
!! ! ..! ..!|||||| |||| || | | | ||||||||||||| ||
|
||||
Thr***GlnThrSerAACATG-CTGTAGATAGAGCTTCTATAGAAGTACAGTTATTCA
|
||||
667141 : ACTTAGCAAACGTCA : 667199
|
||||
|
||||
500 : CTCAAGAGAATGAGAAA : 516
|
||||
||| | || | |||
|
||||
667200 : AACAAAAAAAAAAAAAA : 667216
|
||||
|
||||
-- completed exonerate analysis
|
||||
315
Tests/Exonerate/exn_22_m_coding2coding.exn
Normal file
315
Tests/Exonerate/exn_22_m_coding2coding.exn
Normal file
@ -0,0 +1,315 @@
|
||||
Command line: [exonerate -m coding2coding ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: coding2coding
|
||||
Raw score: 2151
|
||||
Query range: 1228 -> 1
|
||||
Target range: 1318047 -> 1319274
|
||||
|
||||
1228 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1174
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
1318048 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1318102
|
||||
|
||||
1173 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1117
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
1318103 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1318159
|
||||
|
||||
1116 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1063
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
1318160 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1318213
|
||||
|
||||
1062 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1006
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
1318214 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1318270
|
||||
|
||||
1005 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 949
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
1318271 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 1318327
|
||||
|
||||
948 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 895
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
1318328 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 1318381
|
||||
|
||||
894 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 838
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
1318382 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 1318438
|
||||
|
||||
837 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 781
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
1318439 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 1318495
|
||||
|
||||
780 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 727
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
1318496 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 1318549
|
||||
|
||||
726 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 670
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
1318550 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 1318606
|
||||
|
||||
669 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 613
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
1318607 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 1318663
|
||||
|
||||
612 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 559
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
1318664 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 1318717
|
||||
|
||||
558 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 502
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
1318718 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 1318774
|
||||
|
||||
501 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 445
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
1318775 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 1318831
|
||||
|
||||
444 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 391
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
1318832 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 1318885
|
||||
|
||||
390 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 334
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
1318886 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 1318942
|
||||
|
||||
333 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 277
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
1318943 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 1318999
|
||||
|
||||
276 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 223
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
1319000 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 1319053
|
||||
|
||||
222 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 166
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
1319054 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 1319110
|
||||
|
||||
165 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 109
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
1319111 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 1319167
|
||||
|
||||
108 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 55
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
1319168 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 1319221
|
||||
|
||||
54 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 2
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
1319222 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 1319274
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: coding2coding
|
||||
Raw score: 2106
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 55
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319221
|
||||
|
||||
56 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
1319220 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 166
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319110
|
||||
|
||||
167 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 223
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
1319109 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319053
|
||||
|
||||
224 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
1319052 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 334
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318942
|
||||
|
||||
335 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 391
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
1318941 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318885
|
||||
|
||||
392 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
1318884 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 502
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318774
|
||||
|
||||
503 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 559
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
1318773 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318717
|
||||
|
||||
560 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
1318716 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 670
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318606
|
||||
|
||||
671 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 727
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
1318605 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318549
|
||||
|
||||
728 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
1318548 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 838
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318438
|
||||
|
||||
839 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 895
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
1318437 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318381
|
||||
|
||||
896 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
1318380 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1006
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318270
|
||||
|
||||
1007 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1063
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
1318269 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318213
|
||||
|
||||
1064 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
1318212 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1174
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318102
|
||||
|
||||
1175 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
1318101 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: coding2coding
|
||||
Raw score: 116
|
||||
Query range: 1065 -> 1224
|
||||
Target range: 255638 -> 255794
|
||||
|
||||
1066 : TGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACATAG : 1123
|
||||
CysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspIleA
|
||||
||+! .!.||| !!:...||+:!::!:! ||+|||||+|||...:!:||+:!:|
|
||||
CysSerGluIleTrpAspArgIleThrThrHisProLysTyrSerAspIleAspValA
|
||||
255639 : TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAATACTCAGATATTGATGTCG : 255696
|
||||
|
||||
1124 : ATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAAATAGT : 1180
|
||||
spAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLysIleVa
|
||||
||! !|||||+++|||++||!!: ||||||||||||:!!!!: :!:||
|
||||
spGlyLeuCysSerGluLeuMetAlaLysAlaLysCysSerGluArg<->GlyValVa
|
||||
255697 : ATGGTTTATGTTCCGAGCTAATGGCAAAGGCAAAATGTTCAGAAAGA<->GGGGTTGT : 255750
|
||||
|
||||
1181 : AGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC : 1224
|
||||
lValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeu
|
||||
+:!!!!.||+...|||:!:||+ |||+|| !!::!!.:!:
|
||||
lIleAsnAlaGluAspValGlnLeuAlaLeuAsnLysHisMet
|
||||
255751 : CATCAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG : 255794
|
||||
|
||||
-- completed exonerate analysis
|
||||
315
Tests/Exonerate/exn_22_m_coding2genome.exn
Normal file
315
Tests/Exonerate/exn_22_m_coding2genome.exn
Normal file
@ -0,0 +1,315 @@
|
||||
Command line: [exonerate -m coding2genome ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: coding2genome
|
||||
Raw score: 2151
|
||||
Query range: 1228 -> 1
|
||||
Target range: 1318047 -> 1319274
|
||||
|
||||
1228 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1174
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
1318048 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1318102
|
||||
|
||||
1173 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1117
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
1318103 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1318159
|
||||
|
||||
1116 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1063
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
1318160 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1318213
|
||||
|
||||
1062 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1006
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
1318214 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1318270
|
||||
|
||||
1005 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 949
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
1318271 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 1318327
|
||||
|
||||
948 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 895
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
1318328 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 1318381
|
||||
|
||||
894 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 838
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
1318382 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 1318438
|
||||
|
||||
837 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 781
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
1318439 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 1318495
|
||||
|
||||
780 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 727
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
1318496 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 1318549
|
||||
|
||||
726 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 670
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
1318550 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 1318606
|
||||
|
||||
669 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 613
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
1318607 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 1318663
|
||||
|
||||
612 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 559
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
1318664 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 1318717
|
||||
|
||||
558 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 502
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
1318718 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 1318774
|
||||
|
||||
501 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 445
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
1318775 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 1318831
|
||||
|
||||
444 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 391
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
1318832 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 1318885
|
||||
|
||||
390 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 334
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
1318886 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 1318942
|
||||
|
||||
333 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 277
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
1318943 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 1318999
|
||||
|
||||
276 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 223
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
1319000 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 1319053
|
||||
|
||||
222 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 166
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
1319054 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 1319110
|
||||
|
||||
165 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 109
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
1319111 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 1319167
|
||||
|
||||
108 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 55
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
1319168 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 1319221
|
||||
|
||||
54 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 2
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
1319222 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 1319274
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: coding2genome
|
||||
Raw score: 2106
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 55
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319221
|
||||
|
||||
56 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
1319220 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 166
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319110
|
||||
|
||||
167 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 223
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
1319109 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319053
|
||||
|
||||
224 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
1319052 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 334
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318942
|
||||
|
||||
335 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 391
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
1318941 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318885
|
||||
|
||||
392 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
1318884 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 502
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318774
|
||||
|
||||
503 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 559
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
1318773 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318717
|
||||
|
||||
560 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
1318716 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 670
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318606
|
||||
|
||||
671 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 727
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
1318605 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318549
|
||||
|
||||
728 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
1318548 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 838
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318438
|
||||
|
||||
839 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 895
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
1318437 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318381
|
||||
|
||||
896 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
1318380 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1006
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318270
|
||||
|
||||
1007 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1063
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
1318269 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318213
|
||||
|
||||
1064 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
1318212 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1174
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318102
|
||||
|
||||
1175 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
1318101 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: coding2genome
|
||||
Raw score: 116
|
||||
Query range: 1065 -> 1224
|
||||
Target range: 255638 -> 255794
|
||||
|
||||
1066 : TGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACATAG : 1123
|
||||
CysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspIleA
|
||||
||+! .!.||| !!:...||+:!::!:! ||+|||||+|||...:!:||+:!:|
|
||||
CysSerGluIleTrpAspArgIleThrThrHisProLysTyrSerAspIleAspValA
|
||||
255639 : TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAATACTCAGATATTGATGTCG : 255696
|
||||
|
||||
1124 : ATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAAATAGT : 1180
|
||||
spAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLysIleVa
|
||||
||! !|||||+++|||++||!!: ||||||||||||:!!!!: :!:||
|
||||
spGlyLeuCysSerGluLeuMetAlaLysAlaLysCysSerGluArg<->GlyValVa
|
||||
255697 : ATGGTTTATGTTCCGAGCTAATGGCAAAGGCAAAATGTTCAGAAAGA<->GGGGTTGT : 255750
|
||||
|
||||
1181 : AGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC : 1224
|
||||
lValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeu
|
||||
+:!!!!.||+...|||:!:||+ |||+|| !!::!!.:!:
|
||||
lIleAsnAlaGluAspValGlnLeuAlaLeuAsnLysHisMet
|
||||
255751 : CATCAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG : 255794
|
||||
|
||||
-- completed exonerate analysis
|
||||
185
Tests/Exonerate/exn_22_m_est2genome.exn
Normal file
185
Tests/Exonerate/exn_22_m_est2genome.exn
Normal file
@ -0,0 +1,185 @@
|
||||
Command line: [exonerate -m est2genome ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: est2genome
|
||||
Raw score: 6150
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319220
|
||||
|
||||
57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108
|
||||
|
||||
169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052
|
||||
|
||||
225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940
|
||||
|
||||
337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884
|
||||
|
||||
393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 504
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772
|
||||
|
||||
505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 560
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716
|
||||
|
||||
561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 672
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604
|
||||
|
||||
673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 728
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548
|
||||
|
||||
729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 840
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436
|
||||
|
||||
841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 896
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380
|
||||
|
||||
897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1008
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268
|
||||
|
||||
1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1064
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212
|
||||
|
||||
1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1176
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100
|
||||
|
||||
1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: est2genome
|
||||
Raw score: 439
|
||||
Query range: 0 -> 346
|
||||
Target range: 85010 -> 473201
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAAGC : 58
|
||||
|||| || | |||| | |||||| |||| | | | |||| ||||||||||
|
||||
85011 : ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAACAGG----ATGAAGAAGC : 85059
|
||||
|
||||
59 : AAATGTT >>>> Target Intron 1 >>>> GCTA-AATAAAGATGGAACACC : 86
|
||||
||| | |++ 168908 bp -+|| | ||| || | | |||
|
||||
85060 : AAAAGATgt.........................tgGCGAGGATAGCGA-GCA--ACC : 253993
|
||||
|
||||
87 : TAAGAGGAAGGTGGGCAGACCAGGCAGAAA-AAGGATT--GACTCTGAAGCTAAGAGT : 141
|
||||
|||| ||||| ||| | | ||| ||| | |||| || ||||| |||||
|
||||
253994 : GAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAGCAG : 254051
|
||||
|
||||
142 : AGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGAGATAGGAAAGAAGCCA : 199
|
||||
| |||||||||||| ||| |||| |||||| |||| || | || | || || |
|
||||
254052 : AAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGAGGA : 254109
|
||||
|
||||
200 : AAATGAAGAGTTTGCAAGAGAGGGTA >>>> Target Intron 2 >>>> GAG : 228
|
||||
| |||||| ||| | ||| ||||-- 96824 bp -+| |
|
||||
254110 : AGATGAAGGAATTGGAGAAGAAGGTAca.........................tgGGG : 350962
|
||||
|
||||
229 : TTACTAGAACA--GAAAGATGCGCAGAATA--AGACTACCACGGACTT-TTTACTATG : 281
|
||||
| | || | || |||| | ||||| || ||||| ||| ||| |||
|
||||
350963 : TGATTATATCATTTCTGGATGAG--GAATACCTGAAGACCAC--TCTTCATTAAAATG : 351016
|
||||
|
||||
282 : TTCTTTAAAAAGTTTACTGTCGGAAAT-TACAAAATATAG >>>> Target Intr : 321
|
||||
||||||||||| | | || | ||| || | | | |||-+ 122118 b
|
||||
351017 : TTCTTTAAAAA-TATTCTTTTGGATATATTCTA---CTAGtt................ : 351055
|
||||
|
||||
322 : on 3 >>>> AGCTAAGAATTCTGATGATG-----AAAGAA : 346
|
||||
p ++| |||||||||||| ||| ||||||
|
||||
351056 : .........agATGGAAGAATTCTGATAATGCTGTAAAAGAA : 473201
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence:[revcomp]
|
||||
Model: est2genome
|
||||
Raw score: 263
|
||||
Query range: 25 -> 406
|
||||
Target range: 130198 -> 11338
|
||||
|
||||
26 : AGCAAATATATTTA-GCAGGTGACATGAAGAAGCAAATGTTGCTAA-ATAAAGATG-- : 80
|
||||
| |||| ||| | |||| | | || |||| | | || ||| | || ||
|
||||
130198 : ACCAAAGATAACAAGGCAG--AAAAAGAGGAAGAAGAAATTAATAAGGTTGAGGTGAC : 130143
|
||||
|
||||
81 : ----GAACACCTAAGAGGAAGGTGGGCAGACCAGGCAGAAAAAGGATTGACTCTGAAG : 133
|
||||
||| | | ||| ||| | || |||||||||||| | || |||
|
||||
130142 : CCCAGAAGAGCCAAGCAAAAGCATAGATAACAAGGCAGAAAAAGAA--GAAGAAGAAA : 130087
|
||||
|
||||
134 : CTAAGA--GTAGGAG-GACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGA <<< : 184
|
||||
||| | || | || ||| |||||| || ||| || || ||| ||++
|
||||
130086 : TTAATAAGGTTGAAGTGAC--CCCAGAGGAGCCAAGCAAAAAGA---TTCGGAct... : 130036
|
||||
|
||||
185 : < Target Intron 1 <<<< GATAGGAAAGAAG-CCAAAATGAAGAGTTTGCAA : 216
|
||||
9357 bp -+| || |||||| |||| | ||||| | ||
|
||||
130035 : ......................tcG-TATTGAAGAAGTCCAAGAAGAAGA-TGAAGAA : 120650
|
||||
|
||||
217 : GA-GAGGGTAGAGTTACTAGAACAGAAAGATG-CGCAG <<<< Target Intron : 253
|
||||
|| | | | ||| | |||||| |||| | | ||-- 109125 bp
|
||||
120649 : GATAATGATGGAG-AAGAAGAACAAGAAGAAGAAGAAGaa.................. : 120610
|
||||
|
||||
254 : 2 <<<< AATAAGACTACCACGGACTTTTTACTATGTTCTTTAAAAAGTTTACTGT : 301
|
||||
++||||||| | ||| | |||| | | | | || || | |||
|
||||
120609 : .......acAATAAGAGCAACACAG----TTTA-TCTTATATGTA-----TTCAATGT : 11449
|
||||
|
||||
302 : CGGAAATTACAAAATATAGAGCT--AAGA--ATTCTGATGATGAAAGAATATTAGCCT : 355
|
||||
| ||| |||||||||||| | || | |||| | || || || || |||
|
||||
11448 : -ATAGATTTCAAAATATAGAGTTTAAATATCATTCAAAATATTCAATAAATTTTTCCT : 11392
|
||||
|
||||
356 : TCCTCGA-TGA-TCTGCAAGAACAACAGAAAAGGGAAAACGAAAAAGGAACAA : 406
|
||||
| | | | | | | || | | || || |||||||| || ||||
|
||||
11391 : TTGAAAATTTAGGCCACTAAAAAATTATAAGAGCCAAAACGAAGTAGATACAA : 11339
|
||||
|
||||
-- completed exonerate analysis
|
||||
207
Tests/Exonerate/exn_22_m_genome2genome.exn
Normal file
207
Tests/Exonerate/exn_22_m_genome2genome.exn
Normal file
@ -0,0 +1,207 @@
|
||||
Command line: [exonerate -m genome2genome ../intron.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: genome2genome
|
||||
Raw score: 2641
|
||||
Query range: 529 -> 0
|
||||
Target range: 1319997 -> 1319468
|
||||
|
||||
529 : TGG : 474
|
||||
ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
|
||||
1319997 : TGG : 1319942
|
||||
|
||||
473 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA : 418
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319941 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA : 1319886
|
||||
|
||||
417 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA : 362
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319885 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA : 1319830
|
||||
|
||||
361 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC : 306
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319829 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC : 1319774
|
||||
|
||||
305 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA : 250
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319773 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA : 1319718
|
||||
|
||||
249 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG : 194
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319717 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG : 1319662
|
||||
|
||||
193 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG : 138
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319661 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG : 1319606
|
||||
|
||||
137 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG : 82
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319605 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG : 1319550
|
||||
|
||||
81 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC : 26
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319549 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC : 1319494
|
||||
|
||||
25 : ATGTGATTGTCGGAAAGAACTTTGG : 1
|
||||
|||||||||||||||||||||||||
|
||||
1319493 : ATGTGATTGTCGGAAAGAACTTTGG : 1319469
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: genome2genome
|
||||
Raw score: 2641
|
||||
Query range: 0 -> 529
|
||||
Target range: 1319468 -> 1319997
|
||||
|
||||
1 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319469 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG : 1319524
|
||||
|
||||
57 : TGG : 112
|
||||
CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
|
||||
1319525 : TGG : 1319580
|
||||
|
||||
113 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319581 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA : 1319636
|
||||
|
||||
169 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319637 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA : 1319692
|
||||
|
||||
225 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319693 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC : 1319748
|
||||
|
||||
281 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319749 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT : 1319804
|
||||
|
||||
337 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319805 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT : 1319860
|
||||
|
||||
393 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT : 448
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319861 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT : 1319916
|
||||
|
||||
449 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG : 504
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319917 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG : 1319972
|
||||
|
||||
505 : GCAACAAGATAAAGAGATAAGGGAT : 529
|
||||
|||||||||||||||||||||||||
|
||||
1319973 : GCAACAAGATAAAGAGATAAGGGAT : 1319997
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
|
||||
Target: gi|330443489|ref|NC_001135.5| Saccharomyces cerevisiae S288c chromosome III, complete sequence
|
||||
Model: genome2genome
|
||||
Raw score: 267
|
||||
Query range: 491 -> 162
|
||||
Target range: 23668 -> 115569
|
||||
|
||||
491 : CCCTTTAAATGGAGATTACAAACTAGCGA >>>> Target Intron 1 >>>> : 462
|
||||
|| | ||| | ||| ||||| | | |++ 8983 bp +-
|
||||
23669 : CCGCTGAAAGGAAGAGAACAAAGTTACAAgt.........................aa : 32679
|
||||
|
||||
461 : AACTGCAGAAAAGGAAAGCCTCCAAAACTACT--GC-CAGGGTAAAAAGTGA >>>> : 413
|
||||
||||||||||||| | || ||| ||| || ||||||| || ||-+
|
||||
32680 : AACTGCAGAAAAGACTGGTATCTTGAACGACTTGGCGAAGGGTAAGAAAAGAat.... : 32735
|
||||
|
||||
412 : Target Intron 2 >>>> AACTGGGAA--ACG-ACAT-AAAGAAGAGCAAATT : 383
|
||||
9555 bp +-||| || || || || | ||||||||||||||
|
||||
32736 : .....................atAAC-GGTAATCTCGAACTTCAAAGAAGAGCAAATG : 42321
|
||||
|
||||
382 : {A} {CC}AAA : 358
|
||||
AAA{T} >>>> Target Intron 3 >>>> {hr}LysATGAGCGATGAAAATA
|
||||
|| { }++ 55423 bp ++{ } ! ||| ||||||||||
|
||||
AAC{L}gt.........................ag{eu}AspTTGAATGATGAAAATA
|
||||
42322 : {C} {TG}GAT : 97769
|
||||
|
||||
357 : AGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATACAAT > : 302
|
||||
|||| | | | | ||| | ||||| | || | || |||||| | |+-
|
||||
97770 : AGAGAA---ATTTATTAGTCATATTCAGTGATTATGTGGTTTTCATCAATATACTgg. : 97824
|
||||
|
||||
301 : >>> Target Intron 4 >>>> TTTTCTTTACTAAC-TCGAGGAAGAGTGAGGT : 272
|
||||
17598 bp ++| || || | | | |||||| |||| |
|
||||
97825 : ........................agTCTTGAAGACCAGCATGTAGGAAG-GTGATGA : 115450
|
||||
|
||||
271 : TTTCTTCC---ATGAATTGCAGCTATTG---T-TAAGGCGTCTGAC-ATAGTATGTAA : 222
|
||||
| | ||| | ||||| | ||||| | ||| |||| ||| || ||
|
||||
115451 : TATGCTCCGTAAATAATTGGAAATATTGAGATATAATAACGATGACAATACTA-ACAA : 115507
|
||||
|
||||
221 : TTGTGCCA--TGATATACATGTTTTGTGTGTGTACATTTGAATATATATATTTAC-TA : 167
|
||||
|| | ||| | | ||| ||| | ||||||||||||| | | ||
|
||||
115508 : AAGTAATAGGTGAGCTCCGCCAATTGATTGTTTTGTTTTGAATATATATTGATGCTTA : 115565
|
||||
|
||||
166 : ACAA : 163
|
||||
||||
|
||||
115566 : ACAA : 115569
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
|
||||
Target: gi|330443667|ref|NC_001143.9| Saccharomyces cerevisiae S288c chromosome XI, complete sequence:[revcomp]
|
||||
Model: genome2genome
|
||||
Raw score: 267
|
||||
Query range: 529 -> 78
|
||||
Target range: 641760 -> 71883
|
||||
|
||||
529 : ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCCCTTTAAATGGAGATTACA : 472
|
||||
|||||||||||||| ||| ||||| |||| || | || || ||
|
||||
641760 : ATCCCTTATCTCTTCTAAAGATTGTGTGGTT---TTTT--CTATGCATATTTTTTCCA : 641708
|
||||
|
||||
471 : ga ag : 385
|
||||
A---ACTAGCGAA-ACTGCAGAAAAG+->>>> Joint Intron 1 >>>>++CAAA
|
||||
| || || || || || | ||| 61 bp // 154295 bp |||
|
||||
ACCTTCTTGCCAATTCTTCA-ACAAG-+>>>> Joint Intron 1 >>>>++CAAT
|
||||
641707 : tt ag : 487384
|
||||
|
||||
384 : TTAAAACCAAAATGAGCGATGAAAATAAGAGTACGCGTATGTCAGTTAATC-TCAGTC : 328
|
||||
|||| ||||| |||||||||| |||| | | |||| | ||||| | ||| |
|
||||
487383 : TTAACACCAAGATGAGCGATG-----AAGA-TTC---TATG-CTGTTAAACTTCACTA : 487336
|
||||
|
||||
327 : gt ga : 263
|
||||
ACAATTTT++>>>> Joint Intron 2 >>>>--GGAAGAGTGAGGTTTTCTTCCA
|
||||
|||| 35 bp // 101120 bp |||| | | || | | | |
|
||||
CCAATGAG+->>>> Joint Intron 2 >>>>++GGAACATAAAAATTCTGTCCTA
|
||||
487335 : ga ag : 386186
|
||||
|
||||
262 : TGCCATGATATAC : 206
|
||||
T-GAATTGCAGCTATTGTTAAGGCGTCTGACATAGTATGTAATTGCysHisAspIleH
|
||||
| || | || |||| || || || | || || |||| ||| ! ! .!.||+
|
||||
TCAAAATTCAATAATTG-TACAGCTTC-CA-ATTGTGTGTACTTGValLysGlnIleG
|
||||
386185 : GTCAAACAAATCG : 386131
|
||||
|
||||
205 : ATGTT{TT} >>>> Target Intron 1 >>>> {G}TGTGTGTACATT : 182
|
||||
isVal{Le} {u}CysValTyrIleTG-AA
|
||||
{::} 177446 bp {:} ! !:: || ||
|
||||
lyHis{Il}++ ++{e}LysGlyPhe***TGAAA
|
||||
386130 : GACAC{AT}gt.........................ag{C}AAAGGATTTTGA : 208660
|
||||
|
||||
181 : ga ag : 105
|
||||
TATATATATTTACTAACAAG+->>>> Joint Intron 3 >>>>++TAAAGATGCT
|
||||
|||||||||||||| | | 47 bp // 136722 bp |||||| |
|
||||
TATATATATTTACTTAGAGT++>>>> Joint Intron 3 >>>>++AAAAGATTTT
|
||||
208659 : gt ag : 71908
|
||||
|
||||
104 : CTGGACAAGTACCAGTTGGAAAGAGA : 79
|
||||
|| || | | ||||||||||||||
|
||||
71907 : CT--ACGACTTGCAGTTGGAAAGAGA : 71884
|
||||
|
||||
-- completed exonerate analysis
|
||||
233
Tests/Exonerate/exn_22_m_ner.exn
Normal file
233
Tests/Exonerate/exn_22_m_ner.exn
Normal file
@ -0,0 +1,233 @@
|
||||
Command line: [exonerate -m ner ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: NER:affine:local:dna2dna
|
||||
Raw score: 6150
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319220
|
||||
|
||||
57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108
|
||||
|
||||
169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052
|
||||
|
||||
225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940
|
||||
|
||||
337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884
|
||||
|
||||
393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 504
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772
|
||||
|
||||
505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 560
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716
|
||||
|
||||
561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 672
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604
|
||||
|
||||
673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 728
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548
|
||||
|
||||
729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 840
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436
|
||||
|
||||
841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 896
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380
|
||||
|
||||
897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1008
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268
|
||||
|
||||
1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1064
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212
|
||||
|
||||
1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1176
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100
|
||||
|
||||
1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443681|ref|NC_001144.5| Saccharomyces cerevisiae S288c chromosome XII, complete sequence
|
||||
Model: NER:affine:local:dna2dna
|
||||
Raw score: 502
|
||||
Query range: 110 -> 1230
|
||||
Target range: 297910 -> 318994
|
||||
|
||||
111 : CAGAAAA--< 31 >--CTGCCCAGAAT--< 10 >--AACGAGCGTTCCG- : 184
|
||||
| |||||--< NER 1 >--| ||||| | |--< NER 2 >--||| | ||||||-
|
||||
297911 : CTGAAAA--< 29 >--CCGCCCAAAGT--< 13 >--AACTGGAGTTCCG- : 297993
|
||||
|
||||
185 : -< 2 >--ATAGGAAAGAAGC--< 30 >--GTTA-CTAGAAC-AGAAAG- : 246
|
||||
-< NER 3 >--|| || |||| ||--< NER 4 >--|||| | ||||| | ||||-
|
||||
297994 : -< 9 >--ATTGG-AAGATGC--< 15 >--GTTATCAAGAACAATAAAG- : 298050
|
||||
|
||||
247 : -< 11 >--AAGACT--< 5 >--GGACTTTTTACTATGTTC--< 12 : 286
|
||||
-< NER 5 >--||||||--< NER 6 >--| ||| || ||| | ||--< NER 7
|
||||
298051 : -< 11 >--AAGACT--< 10 >--GCACTATTCACTGTCCTC--< 12 : 298096
|
||||
|
||||
287 : >--ACTGTCGGAAAT--< 1 >--ACAAAATATAGAGCTAA--GAAT-TCTGA : 335
|
||||
>--|| || ||||--< NER 8 >--|||||| | | |||| | || | | |||
|
||||
298097 : >--ACATTCTCAAAT--< 10 >--ACAAAA-AAACAGCTGATTGATTATTTGA : 298145
|
||||
|
||||
336 : TGAT--< 369 >--AACTACTT--< 12 >--TGAACG--< 10 >- : 736
|
||||
||| --< NER 9 >--| || |||--< NER 10 >--|||| |--< NER 11 >-
|
||||
298146 : TGAA--< 20288 >--AGCTTCTT--< 9 >--TGAAAG--< 16 >- : 318477
|
||||
|
||||
737 : -GAAAAAATAGATACGTCAGCATG--< 11 >--TTGACCAAAAGTATCTTCCA : 798
|
||||
-||| ||||| || | || | ||--< NER 12 >--||||| | | |||| |
|
||||
318478 : -GAATAAATACAT--GGCACCTTG--< 6 >--TTGACATTCAATGCCTTCTA : 318523
|
||||
|
||||
799 : TACGAG--< 12 >--ACTTT--< 11 >--TGCTTCCCCTTGC--< : 847
|
||||
| |||--< NER 13 >--|||||--< NER 14 >--| | ||||||| |--< NE
|
||||
318524 : -AAGAG--< 37 >--ACTTT--< 41 >--TTCCTCCCCTTCC--< : 318631
|
||||
|
||||
848 : 44 >--GGACCAA--< 19 >--ATCAAATGCGACTTAA--< 9 >- : 933
|
||||
R 15 >--|||| ||--< NER 16 >--||||||| | || ||--< NER 17 >-
|
||||
318632 : 6 >--GGACGAA--< 2 >--ATCAAAT-CAACCAAA--< 5 >- : 318660
|
||||
|
||||
934 : -ACCTGT--< 7 >--GAAATC--< 1 >--CTAGCTTC--< 11 : 970
|
||||
-||||||--< NER 18 >--||||||--< NER 19 >--|||| |||--< NER 2
|
||||
318661 : -ACCTGT--< 16 >--GAAATC--< 4 >--CTAGTTTC--< 9 : 318709
|
||||
|
||||
971 : >--TGGCTGCTTCTCAT--< 13 >--GAACCCAAT--< 1 >--TG : 1018
|
||||
0 >--|| || | ||||||--< NER 21 >--||| ||| |--< NER 22 >--||
|
||||
318710 : >--TGTCT-CATCTCAT--< 4 >--GAATCCAGT--< 8 >--TG : 318744
|
||||
|
||||
1019 : AAGC--< 2 >--TTGAACACATT-AGCAG--< 7 >--TCGAATGGA : 1056
|
||||
|||--< NER 23 >--|||| |||||| | |||--< NER 24 >--|||||| |
|
||||
318745 : TAGC--< 7 >--TTGACCACATTCACCAG--< 15 >--TCGAAT-GC : 318795
|
||||
|
||||
1057 : AAAGCGTCTTGCTACCACATTCTCGAA--< 9 >--TCCCT--< 2 > : 1099
|
||||
|||| || ||| ||||| |||||--< NER 25 >--|||||--< NER 26 >
|
||||
318796 : AAAGAAGCTAGCT-GAACATTATCGAA--< 13 >--TCCCT--< 12 > : 318852
|
||||
|
||||
1100 : --CAAAATATTCATCGTTGGA--< 3 >--AGATGATTT--< 3 >-- : 1132
|
||||
--|||||| ||| || | | |--< NER 27 >--|||| ||||--< NER 28 >--
|
||||
318853 : --CAAAATTTTCTTCATAGAA--< 19 >--AGAT-ATTT--< 16 >-- : 318914
|
||||
|
||||
1133 : CAGCGA--< 17 >--AATGTACAG--< 2 >--GACTGCAAAA--< : 1179
|
||||
|||| |--< NER 29 >--| ||||| |--< NER 30 >--|||| |||||--< N
|
||||
318915 : CAGCTA--< 5 >--ACTGTACCG--< 11 >--GACTTCAAAA--< : 318960
|
||||
|
||||
1180 : 10 >--AGCTCGCGACTTA--< 10 >--TGGTTAGACAGCTCCTGTAG : 1230
|
||||
ER 31 >--|||| |||| |--< NER 32 >--|| | ||||||||||||||
|
||||
318961 : 5 >--AGCTATAGACTCA--< 2 >--TGATAGGACAGCTCCTGTAG : 318994
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: NER:affine:local:dna2dna
|
||||
Raw score: 440
|
||||
Query range: 509 -> 1192
|
||||
Target range: 183946 -> 184603
|
||||
|
||||
510 : TGAGA--< 23 >--TGGAACGCTC--< 20 >--GATTCTCCCCCCGGAAA : 584
|
||||
|||||--< NER 1 >--|| ||| ||--< NER 2 >--|| ||| | | |||
|
||||
183947 : TGAGA--< 26 >--TGAAACTGTC--< 15 >--GAAGCTCTTTCAGAAAA : 184019
|
||||
|
||||
585 : TCGAACAGGTG--< 12 >--GTGACGAAAG--< 19 >--CCAGATTTCAG : 647
|
||||
| ||| |||--< NER 3 >--|||| || ||--< NER 4 >--|| |||| ||
|
||||
184020 : GCCAACTCGTG--< 14 >--GTGAAGACAG--< 12 >--CCGGATTACAA : 184077
|
||||
|
||||
648 : TCT--< 17 >--ATAGACAGACTGGTC--< 1 >--AGAAGCT-TTAGAT : 696
|
||||
|||--< NER 5 >--| ||| || | |||--< NER 6 >--|||| || ||||
|
||||
184078 : TCT--< 12 >--AGAGAAAGGCAAGTC--< 4 >--AGAAACTGGCAGAT : 184125
|
||||
|
||||
697 : -TACGACATTCATAACTACTTTC--< 19 >--GACCGCTGA--< 2 >-- : 748
|
||||
| ||| || | || | ||||--< NER 7 >--| |||||||--< NER 8 >--
|
||||
184126 : CTTGGAC-TTGAAAAGGAGTTTC--< 22 >--GGCCGCTGA--< 12 >-- : 184191
|
||||
|
||||
749 : AAAT--AGATACGTCAGCAT--< 11 >--ATTGACCAAAAGTA--< 6 : 793
|
||||
|||| |||| | |||||||--< NER 9 >--||| || |||| ||--< NER 10
|
||||
184192 : AAATGCAGAT-CATCAGCAT--< 2 >--ATT-ACGAAAACTA--< 15 : 184240
|
||||
|
||||
794 : >--ATACGAGACAGA--< 6 >--TACTTTATTCCCCAGCGT--< 10 : 835
|
||||
>--| || ||| |||--< NER 11 >--|||| || ||||| |--< NER 12
|
||||
184241 : >--AAACCAGAAAGA--< 20 >--TACTAGGTT-ACCAGCTT--< 11 : 184300
|
||||
|
||||
836 : >--GCTGT--< 13 >--AATAATATTTGCAACCGCAAG--< 20 >--T : 903
|
||||
>--|||||--< NER 13 >--|| || | || || | || |--< NER 14 >--|
|
||||
184301 : >--GCTGT--< 11 >--AAGAAGACATGGAAACCCAGG--< 10 >--T : 184347
|
||||
|
||||
904 : TCAAATAAGGAGATCAA--< 7 >--TTAATAACAAG--< 19 >--TC : 959
|
||||
||||| ||| ||| ||--< NER 15 >--|||| || |||--< NER 16 >--|
|
||||
184348 : TCAAAGAAGAAGAAGAA--< 2 >--TTAAAAAGAAG--< 16 >--TG : 184395
|
||||
|
||||
960 : TCTAGCTTCGGTGCTT-CCGG--TGGCTGCTTCTCATAC--< 15 >--CCAAT : 1015
|
||||
|||| || | ||| |||| || || ||| ||||--< NER 17 >--| |||
|
||||
184396 : TCTA-CTAGAGAACTTGCCGGCAAGGTTGGGTCT-ATAC--< 7 >--CAAAT : 184444
|
||||
|
||||
1016 : CTGAA--< 2 >--AATTGAACA--< 19 >--AATGGAAAAGCGTCTT : 1066
|
||||
||| |--< NER 18 >--||||| | |--< NER 19 >--| ||| |||| ||
|
||||
184445 : CTGGA--< 14 >--AATTGGAAA--< 13 >--ATTGGCAAAG-GTGCC : 184500
|
||||
|
||||
1067 : GCTACCACATTCT--< 20 >--CAAAATATT--< 14 >--GATGATTT : 1130
|
||||
| |||||||| |--< NER 20 >--||| || ||--< NER 21 >--||||||
|
||||
184501 : GAAACCACATTTT--< 2 >--CAAGATGTT--< 18 >--GATGATGC : 184550
|
||||
|
||||
1131 : AT--GCAGCGAA--< 7 >--TCAAGGC--< 13 >--GACTGCAAAAT : 1178
|
||||
|| ||||| |--< NER 22 >--|| ||||--< NER 23 >--||| | |||||
|
||||
184551 : ATCCTCAGCGGA--< 3 >--TCTAGGC--< 6 >--GACGGTAAAAT : 184589
|
||||
|
||||
1179 : AGTAGTCAAAGCTC : 1192
|
||||
|||||||| | |||
|
||||
184590 : AGTAGTCACACCTC : 184603
|
||||
|
||||
-- completed exonerate analysis
|
||||
183
Tests/Exonerate/exn_22_m_protein2dna.exn
Normal file
183
Tests/Exonerate/exn_22_m_protein2dna.exn
Normal file
@ -0,0 +1,183 @@
|
||||
Command line: [exonerate -m protein2dna ../scer_cad1_prot.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: protein2dna:local
|
||||
Raw score: 2105
|
||||
Query range: 0 -> 409
|
||||
Target range: 1319275 -> 1318048
|
||||
|
||||
1 : MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy : 19
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319221
|
||||
|
||||
20 : sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA : 38
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
1319220 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
39 : rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319110
|
||||
|
||||
57 : GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa : 75
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
1319109 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319053
|
||||
|
||||
76 : lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC : 94
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
1319052 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
95 : ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp : 112
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318942
|
||||
|
||||
113 : AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs : 131
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
1318941 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318885
|
||||
|
||||
132 : nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA : 150
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
1318884 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
151 : snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318774
|
||||
|
||||
169 : GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs : 187
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
1318773 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318717
|
||||
|
||||
188 : nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS : 206
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
1318716 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
207 : erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318606
|
||||
|
||||
225 : GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe : 243
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
1318605 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318549
|
||||
|
||||
244 : rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG : 262
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
1318548 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
263 : lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318438
|
||||
|
||||
281 : LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy : 299
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
1318437 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318381
|
||||
|
||||
300 : sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG : 318
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
1318380 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
319 : lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318270
|
||||
|
||||
337 : ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe : 355
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
1318269 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318213
|
||||
|
||||
356 : rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI : 374
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
1318212 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
375 : leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318102
|
||||
|
||||
393 : IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu : 409
|
||||
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu
|
||||
1318101 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTG : 1318049
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: protein2dna:local
|
||||
Raw score: 205
|
||||
Query range: 28 -> 120
|
||||
Target range: 253991 -> 254270
|
||||
|
||||
29 : ProLysArgLysValGlyArgProGlyArgLysArg<->IleAspSerGluAlaLysS : 47
|
||||
||||||!:!|||! !.!!!:! !!.!!!:!|||!:! :!:||| !!|||.!!|||.
|
||||
ProLysLysLysGlySerLysThrSerLysLysGlnAspLeuAspProGluThrLysG
|
||||
253992 : CCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAGC : 254049
|
||||
|
||||
48 : erArgArgThrAlaGlnAsnArgAlaAlaGlnArgAlaPheArgAspArgLysGluAl : 66
|
||||
.!!:!|||||||||||||||||||||||||||||||||||||||!!:|||||||||
|
||||
lnLysArgThrAlaGlnAsnArgAlaAlaGlnArgAlaPheArgGluArgLysGluAr
|
||||
254050 : AGAAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGAG : 254106
|
||||
|
||||
67 : aLysMetLysSerLeuGlnGluArgValGluLeuLeuGluGlnLysAspAlaGlnAsn : 85
|
||||
!|||||||||..!|||:!!:!!!:!|||:!! !||||||...! .!. !||||||
|
||||
gLysMetLysGluLeuGluLysLysValGlnSerLeuGluSerIleGlnGlnGlnAsn
|
||||
254107 : GAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTTTAGAGAGTATTCAGCAGCAAAAT : 254163
|
||||
|
||||
86 : LysThrThrThrAspPheLeuLeuCysSerLeuLysSerLeuLeuSerGluIleThrL : 105
|
||||
:!!..! !.!! !|||||| ! !..!|||! !!!|||:!!!:!|||:!!! !|
|
||||
GluValGluAlaThrPheLeuArgAspGlnLeuIleThrLeuValAsnGluLeuLysL
|
||||
254164 : GAAGTGGAAGCTACTTTTTTGAGGGACCAGTTAATCACTCTGGTGAATGAGTTAAAAA : 254223
|
||||
|
||||
106 : ysTyrArgAlaLysAsnSerAspAspGluArgIleLeuAlaPheLeu : 120
|
||||
|||||||| !!:!!!..!!!:!!|||..!!:!:!:|||! !!:!|||
|
||||
ysTyrArgProGluThrArgAsnAspSerLysValLeuGluTyrLeu
|
||||
254224 : AATATAGACCAGAGACAAGAAATGACTCAAAAGTGCTGGAATATTTA : 254270
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: protein2dna:local
|
||||
Raw score: 116
|
||||
Query range: 355 -> 408
|
||||
Target range: 255638 -> 255794
|
||||
|
||||
356 : CysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspIleA : 375
|
||||
|||! .!.|||! !!!:..!|||!!!!!!! !||||||||||||..!:!!|||:!!|
|
||||
CysSerGluIleTrpAspArgIleThrThrHisProLysTyrSerAspIleAspValA
|
||||
255639 : TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAATACTCAGATATTGATGTCG : 255696
|
||||
|
||||
376 : spAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLysIleVa : 394
|
||||
||! !|||||||||||||||!!: !||||||||||||:!!!!: !:!!||
|
||||
spGlyLeuCysSerGluLeuMetAlaLysAlaLysCysSerGluArg---GlyValVa
|
||||
255697 : ATGGTTTATGTTCCGAGCTAATGGCAAAGGCAAAATGTTCAGAAAGA---GGGGTTGT : 255750
|
||||
|
||||
395 : lValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeu : 408
|
||||
|:!!!!.|||..!|||:!!|||! !|||||| !!:!!!.:!!
|
||||
lIleAsnAlaGluAspValGlnLeuAlaLeuAsnLysHisMet
|
||||
255751 : CATCAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG : 255794
|
||||
|
||||
-- completed exonerate analysis
|
||||
193
Tests/Exonerate/exn_22_m_protein2genome.exn
Normal file
193
Tests/Exonerate/exn_22_m_protein2genome.exn
Normal file
@ -0,0 +1,193 @@
|
||||
Command line: [exonerate -m protein2genome ../scer_cad1_prot.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: protein2genome:local
|
||||
Raw score: 2105
|
||||
Query range: 0 -> 409
|
||||
Target range: 1319275 -> 1318048
|
||||
|
||||
1 : MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy : 19
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319221
|
||||
|
||||
20 : sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA : 38
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
1319220 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
39 : rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319110
|
||||
|
||||
57 : GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa : 75
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
1319109 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319053
|
||||
|
||||
76 : lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC : 94
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
1319052 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
95 : ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp : 112
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318942
|
||||
|
||||
113 : AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs : 131
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
1318941 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318885
|
||||
|
||||
132 : nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA : 150
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
1318884 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
151 : snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318774
|
||||
|
||||
169 : GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs : 187
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
1318773 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318717
|
||||
|
||||
188 : nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS : 206
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
1318716 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
207 : erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318606
|
||||
|
||||
225 : GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe : 243
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
1318605 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318549
|
||||
|
||||
244 : rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG : 262
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
1318548 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
263 : lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318438
|
||||
|
||||
281 : LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy : 299
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
1318437 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318381
|
||||
|
||||
300 : sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG : 318
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
1318380 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
319 : lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318270
|
||||
|
||||
337 : ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe : 355
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
1318269 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318213
|
||||
|
||||
356 : rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI : 374
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
1318212 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
375 : leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318102
|
||||
|
||||
393 : IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu : 409
|
||||
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu
|
||||
1318101 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTG : 1318049
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: protein2genome:local
|
||||
Raw score: 205
|
||||
Query range: 28 -> 120
|
||||
Target range: 253991 -> 254270
|
||||
|
||||
29 : ProLysArgLysValGlyArgProGlyArgLysArg<->IleAspSerGluAlaLysS : 47
|
||||
||||||!:!|||! !.!!!:! !!.!!!:!|||!:! :!:||| !!|||.!!|||.
|
||||
ProLysLysLysGlySerLysThrSerLysLysGlnAspLeuAspProGluThrLysG
|
||||
253992 : CCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAGC : 254049
|
||||
|
||||
48 : erArgArgThrAlaGlnAsnArgAlaAlaGlnArgAlaPheArgAspArgLysGluAl : 66
|
||||
.!!:!|||||||||||||||||||||||||||||||||||||||!!:|||||||||
|
||||
lnLysArgThrAlaGlnAsnArgAlaAlaGlnArgAlaPheArgGluArgLysGluAr
|
||||
254050 : AGAAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGAG : 254106
|
||||
|
||||
67 : aLysMetLysSerLeuGlnGluArgValGluLeuLeuGluGlnLysAspAlaGlnAsn : 85
|
||||
!|||||||||..!|||:!!:!!!:!|||:!! !||||||...! .!. !||||||
|
||||
gLysMetLysGluLeuGluLysLysValGlnSerLeuGluSerIleGlnGlnGlnAsn
|
||||
254107 : GAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTTTAGAGAGTATTCAGCAGCAAAAT : 254163
|
||||
|
||||
86 : LysThrThrThrAspPheLeuLeuCysSerLeuLysSerLeuLeuSerGluIleThrL : 105
|
||||
:!!..! !.!! !|||||| ! !..!|||! !!!|||:!!!:!|||:!!! !|
|
||||
GluValGluAlaThrPheLeuArgAspGlnLeuIleThrLeuValAsnGluLeuLysL
|
||||
254164 : GAAGTGGAAGCTACTTTTTTGAGGGACCAGTTAATCACTCTGGTGAATGAGTTAAAAA : 254223
|
||||
|
||||
106 : ysTyrArgAlaLysAsnSerAspAspGluArgIleLeuAlaPheLeu : 120
|
||||
|||||||| !!:!!!..!!!:!!|||..!!:!:!:|||! !!:!|||
|
||||
ysTyrArgProGluThrArgAsnAspSerLysValLeuGluTyrLeu
|
||||
254224 : AATATAGACCAGAGACAAGAAATGACTCAAAAGTGCTGGAATATTTA : 254270
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: sp|P24813|YAP2_YEAST AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2
|
||||
Target: gi|330443590|ref|NC_001140.6| Saccharomyces cerevisiae S288c chromosome VIII, complete sequence:[revcomp]
|
||||
Model: protein2genome:local
|
||||
Raw score: 122
|
||||
Query range: 37 -> 125
|
||||
Target range: 84646 -> 68450
|
||||
|
||||
38 : ArgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAlaGln : 57
|
||||
!.!:!!!.!:!! ..!!!::!!|||:!!!:!!:!! !|||||||||||||||||||||
|
||||
AsnGluAsnValProAspAspSerLysAlaLysLysLysAlaGlnAsnArgAlaAlaGln
|
||||
84646 : AATGAGAATGTTCCAGATGACTCTAAGGCAAAGAAAAAGGCTCAAAACAGAGCCGCCCAA : 84589
|
||||
|
||||
58 : ArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArg{Va} >>> : 75
|
||||
!:!|||||||||!!:||||||||||||!:!||||||..!||||||!!:!:!{:!}
|
||||
LysAlaPheArgGluArgLysGluAlaArgMetLysGluLeuGlnAspLys{Le}++
|
||||
84588 : AAAGCCTTCAGAGAGAGAAAAGAAGCCAGAATGAAAGAATTACAAGATAAA{TT}gt... : 84531
|
||||
|
||||
76 : > Target Intron 1 >>>> {l}GluLeuLeuGluGlnLysAspAlaGlnAsnLys : 86
|
||||
15932 bp {!}.!. !:!! !.!.!:!||| !!||| !! !
|
||||
+-{u}AsnLysIleLeuAsnArgAspProGlnPheMet
|
||||
84530 : ......................at{A}AACAAGATACTGAACAGGGACCCCCAGTTCATG : 68570
|
||||
|
||||
87 : ThrThrThrAspPheLeuLeuCysSerLeuLysSerLeuLeuSerGluIleThrLysTyr : 106
|
||||
:!!!.!:!!..!|||! !! !||| !! ! !..!! !:!!!:! ||| !||| !!
|
||||
SerAsnSerSerPheHisGlnCysValSerLeuAspSerIleAsnThrIleGluLysAsp
|
||||
68569 : TCGAATTCCAGCTTTCATCAGTGTGTTTCACTAGATTCCATAAACACTATTGAAAAAGAT : 68510
|
||||
|
||||
107 : ArgAlaLysAsnSerAspAspGluArgIleLeuAlaPheLeuAspAspLeuGlnGlu : 125
|
||||
..!! !|||||||||||||||!!: ! !||| ! ! ! ||| !::!|||
|
||||
GluGluLysAsnSerAspAspAspAlaGlyLeuGlnAlaAlaThrAspAlaArgGlu
|
||||
68509 : GAAGAAAAGAATAGTGACGATGATGCTGGTTTGCAGGCCGCCACAGATGCAAGAGAA : 68451
|
||||
|
||||
-- completed exonerate analysis
|
||||
137
Tests/Exonerate/exn_22_m_ungapped.exn
Normal file
137
Tests/Exonerate/exn_22_m_ungapped.exn
Normal file
@ -0,0 +1,137 @@
|
||||
Command line: [exonerate -m ungapped ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: ungapped:dna2dna
|
||||
Raw score: 6150
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 56
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319220
|
||||
|
||||
57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 168
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108
|
||||
|
||||
169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 224
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052
|
||||
|
||||
225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 336
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940
|
||||
|
||||
337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 392
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884
|
||||
|
||||
393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 504
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772
|
||||
|
||||
505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 560
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716
|
||||
|
||||
561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 672
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604
|
||||
|
||||
673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 728
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548
|
||||
|
||||
729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 840
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436
|
||||
|
||||
841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 896
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380
|
||||
|
||||
897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1008
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268
|
||||
|
||||
1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1064
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212
|
||||
|
||||
1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1176
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100
|
||||
|
||||
1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: ungapped:dna2dna
|
||||
Raw score: 233
|
||||
Query range: 121 -> 236
|
||||
Target range: 254031 -> 254146
|
||||
|
||||
122 : TTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTT : 179
|
||||
| || ||||| ||||| | |||||||||||| ||| |||| |||||| |||| ||
|
||||
254032 : TGGATCCTGAAACTAAGCAGAAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTT : 254089
|
||||
|
||||
180 : CCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGTAGAGTTACTAGA : 236
|
||||
| || | || || || |||||| ||| | ||| |||| | ||||
|
||||
254090 : TAGGGAACGTAAGGAGAGGAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTTTAGA : 254146
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
|
||||
Model: ungapped:dna2dna
|
||||
Raw score: 151
|
||||
Query range: 1098 -> 1166
|
||||
Target range: 255671 -> 255739
|
||||
|
||||
1099 : CCAAAATATTCATCGTTGGACATAGATGATTTATGCAGCGAATTAATAATCAAGGCAA : 1156
|
||||
|| ||||| ||| | || | |||| |||||| ||| |||| |||||||
|
||||
255672 : CCGAAATACTCAGATATTGATGTCGATGGTTTATGTTCCGAGCTAATGGCAAAGGCAA : 255729
|
||||
|
||||
1157 : AATGTACAGA : 1166
|
||||
||||| ||||
|
||||
255730 : AATGTTCAGA : 255739
|
||||
|
||||
-- completed exonerate analysis
|
||||
429
Tests/Exonerate/exn_22_m_ungapped_trans.exn
Normal file
429
Tests/Exonerate/exn_22_m_ungapped_trans.exn
Normal file
@ -0,0 +1,429 @@
|
||||
Command line: [exonerate -m ungapped:trans ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
|
||||
Hostname: [blackbriar]
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: ungapped:codon
|
||||
Raw score: 2151
|
||||
Query range: 1228 -> 1
|
||||
Target range: 1318047 -> 1319274
|
||||
|
||||
1228 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1174
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlyAlaVal***ProGluHisSerValSerArgGluLeu***LeuLeuPheCy
|
||||
1318048 : ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTTTG : 1318102
|
||||
|
||||
1173 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1117
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sSerHisLeuTyrIleLeuPro***LeuLeuIleArgCysIleAsnHisLeuCysP
|
||||
1318103 : CAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATGTC : 1318159
|
||||
|
||||
1116 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1063
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
roThrMetAsnIleLeuValGlyArgArgSerLeuArgGluCysGlySerLysThr
|
||||
1318160 : CAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGACG : 1318213
|
||||
|
||||
1062 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1006
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuPheHisSerIleTrpArgCys***CysValGlnLeuLeuGlnIleGlyPheGl
|
||||
1318214 : CTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTCGA : 1318270
|
||||
|
||||
1005 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 949
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uLeuPhe***TyrGluLysGlnProProGluAlaProLysLeuGluIleSerAspS
|
||||
1318271 : ATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGATT : 1318327
|
||||
|
||||
948 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 895
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erThrGlyGlyLeuLeuLeuSerArgIle***SerProTyrLeuAsnMetValTrp
|
||||
1318328 : CAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTTGG : 1318381
|
||||
|
||||
894 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 838
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerArgTyrThrCysGlyCysLysTyrTyrTyrThrGlySerLeuGlnGlnGlyGl
|
||||
1318382 : TCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGGGA : 1318438
|
||||
|
||||
837 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 781
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uAlaArgTrpGlyIleLysTyrHisLeuLeuSerArgMetGluAspThrPheGlyG
|
||||
1318439 : AGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGGTC : 1318495
|
||||
|
||||
780 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 727
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnPheHisIleAspMetLeuThrTyrLeuPhePheGlnArgSerGlyValGlnSer
|
||||
1318496 : AATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGAGT : 1318549
|
||||
|
||||
726 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 670
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AlaGluGluSerSerTyrGluCysArgAsnLeuLysLeuLeuAspGlnSerValTy
|
||||
1318550 : GCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTCTA : 1318606
|
||||
|
||||
669 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 613
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rHisTrpArgGlnAspArgAsp***AsnLeuAlaPheHisTyrHis***TyrPheA
|
||||
1318607 : TCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTTTC : 1318663
|
||||
|
||||
612 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 559
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgHisArgTrp***ArgHisLeuPheAspPheArgGlyGluAsnProThrAsnTrp
|
||||
1318664 : GTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATTGG : 1318717
|
||||
|
||||
558 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 502
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAsnTrpGluArgSerMetSerLeuCysSerThr***LeuSerHisSerLeuGl
|
||||
1318718 : TTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTTGA : 1318774
|
||||
|
||||
501 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 445
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uCysAlaAlaValLeuLeuTyrLeuCysSerGlnSerCysPheHisLeuAsn***A
|
||||
1318775 : GTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTAGG : 1318831
|
||||
|
||||
444 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 391
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
laMetAlaIleProLeuGlnProCys***LeuLeuTyrLeuPheLeuPheArgPhe
|
||||
1318832 : CGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTTTT : 1318885
|
||||
|
||||
390 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 334
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ProPheSerValValLeuAlaAspHisArgGlyArgLeuIlePhePheHisHisGl
|
||||
1318886 : CCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCATCA : 1318942
|
||||
|
||||
333 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 277
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nAsnSer***LeuTyrIleLeu***PheProThrValAsnPheLeuLysAsnIleV
|
||||
1318943 : GAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACATAG : 1318999
|
||||
|
||||
276 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 223
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
alLysSerProTrp***SerTyrSerAlaHisLeuSerValLeuValThrLeuPro
|
||||
1319000 : TAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTACCC : 1319053
|
||||
|
||||
222 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 166
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerLeuAlaAsnSerSerPheTrpLeuLeuSerTyrLeuGlyThrLeuValGluLe
|
||||
1319054 : TCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAGCT : 1319110
|
||||
|
||||
165 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 109
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uProTyrSerGlyGlnSerSerTyrSer***LeuGlnSerGlnSerPhePheCysL
|
||||
1319111 : GCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTGCC : 1319167
|
||||
|
||||
108 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 55
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
euValCysProProSerSer***ValPheHisLeuTyrLeuAlaThrPheAlaSer
|
||||
1319168 : TGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTTCT : 1319221
|
||||
|
||||
54 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 2
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
SerCysHisLeuLeuAsnIlePheAlaAspLeuSerGluGlyTyrCysPro
|
||||
1319222 : TCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA : 1319274
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
|
||||
Model: ungapped:codon
|
||||
Raw score: 2106
|
||||
Query range: 0 -> 1230
|
||||
Target range: 1319275 -> 1318045
|
||||
|
||||
1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 55
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
MetGlyAsnIleLeuArgLysGlyGlnGlnIleTyrLeuAlaGlyAspMetLysLy
|
||||
1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319221
|
||||
|
||||
56 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 112
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sGlnMetLeuLeuAsnLysAspGlyThrProLysArgLysValGlyArgProGlyA
|
||||
1319220 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164
|
||||
|
||||
113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 166
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgLysArgIleAspSerGluAlaLysSerArgArgThrAlaGlnAsnArgAlaAla
|
||||
1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319110
|
||||
|
||||
167 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 223
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnArgAlaPheArgAspArgLysGluAlaLysMetLysSerLeuGlnGluArgVa
|
||||
1319109 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319053
|
||||
|
||||
224 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 280
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lGluLeuLeuGluGlnLysAspAlaGlnAsnLysThrThrThrAspPheLeuLeuC
|
||||
1319052 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996
|
||||
|
||||
281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 334
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ysSerLeuLysSerLeuLeuSerGluIleThrLysTyrArgAlaLysAsnSerAsp
|
||||
1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318942
|
||||
|
||||
335 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 391
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
AspGluArgIleLeuAlaPheLeuAspAspLeuGlnGluGlnGlnLysArgGluAs
|
||||
1318941 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318885
|
||||
|
||||
392 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 448
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nGluLysGlyThrSerThrAlaValSerLysAlaAlaLysGluLeuProSerProA
|
||||
1318884 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828
|
||||
|
||||
449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 502
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
snSerAspGluAsnMetThrValAsnThrSerIleGluValGlnProHisThrGln
|
||||
1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318774
|
||||
|
||||
503 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 559
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GluAsnGluLysValMetTrpAsnIleGlySerTrpAsnAlaProSerLeuThrAs
|
||||
1318773 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318717
|
||||
|
||||
560 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 616
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
nSerTrpAspSerProProGlyAsnArgThrGlyAlaValThrIleGlyAspGluS
|
||||
1318716 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660
|
||||
|
||||
617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 670
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
erIleAsnGlySerGluMetProAspPheSerLeuAspLeuValSerAsnAspArg
|
||||
1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318606
|
||||
|
||||
671 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 727
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlnThrGlyLeuGluAlaLeuAspTyrAspIleHisAsnTyrPheProGlnHisSe
|
||||
1318605 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318549
|
||||
|
||||
728 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 784
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rGluArgLeuThrAlaGluLysIleAspThrSerAlaCysGlnCysGluIleAspG
|
||||
1318548 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492
|
||||
|
||||
785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 838
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysTyrLeuProTyrGluThrGluAspAspThrLeuPheProSerValLeuPro
|
||||
1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318438
|
||||
|
||||
839 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 895
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuAlaValGlySerGlnCysAsnAsnIleCysAsnArgLysCysIleGlyThrLy
|
||||
1318437 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318381
|
||||
|
||||
896 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 952
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
sProCysSerAsnLysGluIleLysCysAspLeuIleThrSerHisLeuLeuAsnG
|
||||
1318380 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324
|
||||
|
||||
953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1006
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
lnLysSerLeuAlaSerValLeuProValAlaAlaSerHisThrLysThrIleArg
|
||||
1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318270
|
||||
|
||||
1007 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1063
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ThrGlnSerGluAlaIleGluHisIleSerSerAlaIleSerAsnGlyLysAlaSe
|
||||
1318269 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318213
|
||||
|
||||
1064 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1120
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysTyrHisIleLeuGluGluIleSerSerLeuProLysTyrSerSerLeuAspI
|
||||
1318212 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156
|
||||
|
||||
1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1174
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leAspAspLeuCysSerGluLeuIleIleLysAlaLysCysThrAspAspCysLys
|
||||
1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318102
|
||||
|
||||
1175 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1230
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
IleValValLysAlaArgAspLeuGlnSerAlaLeuValArgGlnLeuLeu***
|
||||
1318101 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046
|
||||
|
||||
|
||||
C4 Alignment:
|
||||
------------
|
||||
Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds:[revcomp]
|
||||
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
|
||||
Model: ungapped:codon
|
||||
Raw score: 2072
|
||||
Query range: 1230 -> 0
|
||||
Target range: 1318045 -> 1319275
|
||||
|
||||
1230 : CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTT : 1176
|
||||
LeuGlnGluLeuSerAsnGlnSerThrLeu***ValAlaSerPheAspTyrTyrPh
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuGlnGluLeuSerAsnGlnSerThrLeu***ValAlaSerPheAspTyrTyrPh
|
||||
1318046 : CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGCTTTGACTACTATTT : 1318100
|
||||
|
||||
1175 : TGCAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATG : 1119
|
||||
eAlaValIleCysThrPheCysLeuAspTyr***PheAlaAla***IleIleTyrV
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
eAlaValIleCysThrPheCysLeuAspTyr***PheAlaAla***IleIleTyrV
|
||||
1318101 : TGCAGTCATCTGTACATTTTGCCTTGATTATTAATTCGCTGCATAAATCATCTATG : 1318157
|
||||
|
||||
1118 : TCCAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGA : 1065
|
||||
alGlnArg***IlePheTrp***GlyGlyAspLeuPheGluAsnValValAlaArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
alGlnArg***IlePheTrp***GlyGlyAspLeuPheGluAsnValValAlaArg
|
||||
1318158 : TCCAACGATGAATATTTTGGTAGGGAGGAGATCTCTTCGAGAATGTGGTAGCAAGA : 1318211
|
||||
|
||||
1064 : CGCTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTC : 1008
|
||||
ArgPheSerIleArgTyrGlyAlaAlaAsnValPheAsnCysPheArgLeuGlySe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ArgPheSerIleArgTyrGlyAlaAlaAsnValPheAsnCysPheArgLeuGlySe
|
||||
1318212 : CGCTTTTCCATTCGATATGGCGCTGCTAATGTGTTCAATTGCTTCAGATTGGGTTC : 1318268
|
||||
|
||||
1007 : GAATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGA : 951
|
||||
rAsnCysPheSerMetArgSerSerHisArgLysHisArgSer***ArgPheLeuI
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rAsnCysPheSerMetArgSerSerHisArgLysHisArgSer***ArgPheLeuI
|
||||
1318269 : GAATTGTTTTAGTATGAGAAGCAGCCACCGGAAGCACCGAAGCTAGAGATTTCTGA : 1318325
|
||||
|
||||
950 : TTCAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTT : 897
|
||||
leGlnGlnValAlaCysTyr***ValAlaPheAspLeuLeuIle***ThrTrpPhe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
leGlnGlnValAlaCysTyr***ValAlaPheAspLeuLeuIle***ThrTrpPhe
|
||||
1318326 : TTCAACAGGTGGCTTGTTATTAAGTCGCATTTGATCTCCTTATTTGAACATGGTTT : 1318379
|
||||
|
||||
896 : GGTCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGG : 840
|
||||
GlyProAspThrLeuAlaValAlaAsnIleIleThrLeuAlaProTyrSerLysGl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
GlyProAspThrLeuAlaValAlaAsnIleIleThrLeuAlaProTyrSerLysGl
|
||||
1318380 : GGTCCCGATACACTTGCGGTTGCAAATATTATTACACTGGCTCCCTACAGCAAGGG : 1318436
|
||||
|
||||
839 : GAAGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGG : 783
|
||||
yLysHisAlaGlyGlu***SerIleIlePheCysLeuValTrpLysIleLeuLeuV
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
yLysHisAlaGlyGlu***SerIleIlePheCysLeuValTrpLysIleLeuLeuV
|
||||
1318437 : GAAGCACGCTGGGGAATAAAGTATCATCTTCTGTCTCGTATGGAAGATACTTTTGG : 1318493
|
||||
|
||||
782 : TCAATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGA : 729
|
||||
alAsnPheThrLeuThrCys***ArgIleTyrPhePheSerGlyGlnAlaPheArg
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
alAsnPheThrLeuThrCys***ArgIleTyrPhePheSerGlyGlnAlaPheArg
|
||||
1318494 : TCAATTTCACATTGACATGCTGACGTATCTATTTTTTCAGCGGTCAGGCGTTCAGA : 1318547
|
||||
|
||||
728 : GTGCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTC : 672
|
||||
ValLeuArgLysValValMetAsnValValIle***SerPhe***ThrSerLeuSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ValLeuArgLysValValMetAsnValValIle***SerPhe***ThrSerLeuSe
|
||||
1318548 : GTGCTGAGGAAAGTAGTTATGAATGTCGTAATCTAAAGCTTCTAGACCAGTCTGTC : 1318604
|
||||
|
||||
671 : TATCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTT : 615
|
||||
rIleIleGlyAspLysIleGluThrGluIleTrpHisPheThrThrIleAsnThrP
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rIleIleGlyAspLysIleGluThrGluIleTrpHisPheThrThrIleAsnThrP
|
||||
1318605 : TATCATTGGAGACAAGATCGAGACTGAAATCTGGCATTTCACTACCATTAATACTT : 1318661
|
||||
|
||||
614 : TCGTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATT : 561
|
||||
heValThrAspGlyAsnGlyThrCysSerIleSerGlyGlyArgIleProArgIle
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
heValThrAspGlyAsnGlyThrCysSerIleSerGlyGlyArgIleProArgIle
|
||||
1318662 : TCGTCACCGATGGTAACGGCACCTGTTCGATTTCCGGGGGGAGAATCCCACGAATT : 1318715
|
||||
|
||||
560 : GGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTT : 504
|
||||
Gly***ThrGlySerValPro***AlaTyrValProHisAsnPheLeuIleLeuLe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
Gly***ThrGlySerValPro***AlaTyrValProHisAsnPheLeuIleLeuLe
|
||||
1318716 : GGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACATAACTTTCTCATTCTCTT : 1318772
|
||||
|
||||
503 : GAGTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTA : 447
|
||||
uSerValArgLeuTyrPheTyrThrCysValHisSerHisValPheIle***IleA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
uSerValArgLeuTyrPheTyrThrCysValHisSerHisValPheIle***IleA
|
||||
1318773 : GAGTGTGCGGCTGTACTTCTATACTTGTGTTCACAGTCATGTTTTCATCTGAATTA : 1318829
|
||||
|
||||
446 : GGCGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTT : 393
|
||||
rgArgTrpGlnPheLeuCysSerLeuAlaAsnCysCysThrCysSerPhePheVal
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rgArgTrpGlnPheLeuCysSerLeuAlaAsnCysCysThrCysSerPhePheVal
|
||||
1318830 : GGCGATGGCAATTCCTTTGCAGCCTTGCTAACTGCTGTACTTGTTCCTTTTTCGTT : 1318883
|
||||
|
||||
392 : TTCCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCAT : 336
|
||||
PheProPheLeuLeuPheLeuGlnIleIleGluGluGly***TyrSerPheIleIl
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
PheProPheLeuLeuPheLeuGlnIleIleGluGluGly***TyrSerPheIleIl
|
||||
1318884 : TTCCCTTTTCTGTTGTTCTTGCAGATCATCGAGGAAGGCTAATATTCTTTCATCAT : 1318940
|
||||
|
||||
335 : CAGAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACAT : 279
|
||||
eArgIleLeuSerSerIlePheCysAsnPheArgGln***ThrPhe***ArgThr*
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
eArgIleLeuSerSerIlePheCysAsnPheArgGln***ThrPhe***ArgThr*
|
||||
1318941 : CAGAATTCTTAGCTCTATATTTTGTAATTTCCGACAGTAAACTTTTTAAAGAACAT : 1318997
|
||||
|
||||
278 : AGTAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTAC : 225
|
||||
*****LysValArgGlySerLeuIleLeuArgIlePheLeuPhe******LeuTyr
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
*****LysValArgGlySerLeuIleLeuArgIlePheLeuPhe******LeuTyr
|
||||
1318998 : AGTAAAAAGTCCGTGGTAGTCTTATTCTGCGCATCTTTCTGTTCTAGTAACTCTAC : 1319051
|
||||
|
||||
224 : CCTCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAG : 168
|
||||
ProLeuLeuGlnThrLeuHisPheGlyPhePheProIleSerGluArgSerLeuSe
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
ProLeuLeuGlnThrLeuHisPheGlyPhePheProIleSerGluArgSerLeuSe
|
||||
1319052 : CCTCTCTTGCAAACTCTTCATTTTGGCTTCTTTCCTATCTCGGAACGCTCGTTGAG : 1319108
|
||||
|
||||
167 : CTGCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTG : 111
|
||||
rCysProIleLeuGlySerProProThrLeuSerPheArgValAsnProPheSerA
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
rCysProIleLeuGlySerProProThrLeuSerPheArgValAsnProPheSerA
|
||||
1319109 : CTGCCCTATTCTGGGCAGTCCTCCTACTCTTAGCTTCAGAGTCAATCCTTTTTCTG : 1319165
|
||||
|
||||
110 : CCTGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTT : 57
|
||||
laTrpSerAlaHisLeuProLeuArgCysSerIlePheIle***GlnHisLeuLeu
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
laTrpSerAlaHisLeuProLeuArgCysSerIlePheIle***GlnHisLeuLeu
|
||||
1319166 : CCTGGTCTGCCCACCTTCCTCTTAGGTGTTCCATCTTTATTTAGCAACATTTGCTT : 1319219
|
||||
|
||||
56 : CTTCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT : 1
|
||||
LeuHisValThrCys***IleTyrLeuLeuThrPheProLysAspIleAlaHis
|
||||
||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
||||
LeuHisValThrCys***IleTyrLeuLeuThrPheProLysAspIleAlaHis
|
||||
1319220 : CTTCATGTCACCTGCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT : 1319275
|
||||
|
||||
-- completed exonerate analysis
|
||||
7
Tests/Exonerate/exn_22_o_vulgar.exn
Normal file
7
Tests/Exonerate/exn_22_o_vulgar.exn
Normal file
@ -0,0 +1,7 @@
|
||||
Command line: [exonerate -m genome2genome ../intron.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showalignment no --showvulgar yes --showcigar no]
|
||||
Hostname: [blackbriar]
|
||||
vulgar: sacCer3_dna 529 0 - gi|330443520|ref|NC_001136.10| 1319997 1319468 - 2641 M 26 26 C 3 3 M 500 500
|
||||
vulgar: sacCer3_dna 0 529 + gi|330443520|ref|NC_001136.10| 1319468 1319997 + 2641 M 90 90 C 3 3 M 436 436
|
||||
vulgar: sacCer3_dna 491 162 - gi|330443489|ref|NC_001135.5| 23668 115569 + 267 M 29 29 5 0 2 I 0 8979 3 0 2 M 32 32 G 0 2 M 2 2 G 0 1 M 15 15 5 0 2 I 0 9551 3 0 2 M 3 3 G 1 0 M 5 5 G 0 2 M 3 3 G 0 1 M 4 4 G 0 1 M 18 18 S 1 1 5 0 2 I 0 55419 3 0 2 S 2 2 C 3 3 M 22 22 G 3 0 M 46 46 5 0 2 I 0 17594 3 0 2 M 14 14 G 0 1 M 9 9 G 1 0 M 15 15 G 0 3 M 17 17 G 0 3 M 1 1 G 0 1 M 13 13 G 0 1 M 6 6 G 1 0 M 12 12 G 0 2 M 45 45 G 0 1 M 6 6
|
||||
vulgar: sacCer3_dna 529 78 - gi|330443667|ref|NC_001143.9| 641760 71883 - 267 M 31 31 G 3 0 M 4 4 G 2 0 M 19 19 G 0 3 M 9 9 G 0 1 M 6 6 G 1 0 M 5 5 5 2 2 I 0 154244 I 57 0 I 0 47 3 2 2 M 25 25 G 5 0 M 4 4 G 1 0 M 3 3 G 3 0 M 4 4 G 1 0 M 9 9 G 0 1 M 14 14 5 2 2 I 0 101116 I 31 0 3 2 2 M 23 23 G 0 1 M 15 15 G 1 0 M 9 9 G 1 0 M 2 2 G 1 0 M 14 14 C 18 18 S 2 2 5 0 2 I 0 177442 3 0 2 S 1 1 C 12 12 M 2 2 G 0 1 M 22 22 5 2 2 I 0 136697 I 7 0 I 0 6 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 3 0 I 0 1 I 2 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 I 0 2 I 2 0 I 0 2 I 17 0 3 2 2 M 12 12 G 2 0 M 22 22
|
||||
-- completed exonerate analysis
|
||||
11
Tests/Exonerate/exn_22_o_vulgar_cigar.exn
Normal file
11
Tests/Exonerate/exn_22_o_vulgar_cigar.exn
Normal file
@ -0,0 +1,11 @@
|
||||
Command line: [exonerate -m genome2genome ../intron.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showalignment no --showvulgar yes --showcigar yes]
|
||||
Hostname: [blackbriar]
|
||||
cigar: sacCer3_dna 529 0 - gi|330443520|ref|NC_001136.10| 1319997 1319468 - 2641 M 26 M 3 M 500
|
||||
vulgar: sacCer3_dna 529 0 - gi|330443520|ref|NC_001136.10| 1319997 1319468 - 2641 M 26 26 C 3 3 M 500 500
|
||||
cigar: sacCer3_dna 0 529 + gi|330443520|ref|NC_001136.10| 1319468 1319997 + 2641 M 90 M 3 M 436
|
||||
vulgar: sacCer3_dna 0 529 + gi|330443520|ref|NC_001136.10| 1319468 1319997 + 2641 M 90 90 C 3 3 M 436 436
|
||||
cigar: sacCer3_dna 491 162 - gi|330443489|ref|NC_001135.5| 23668 115569 + 267 M 29 D 8983 M 32 D 2 M 2 D 1 M 15 D 9555 M 3 I 1 M 5 D 2 M 3 D 1 M 4 D 1 M 18 M 1 D 55423 M 5 M 22 I 3 M 46 D 17598 M 14 D 1 M 9 I 1 M 15 D 3 M 17 D 3 M 1 D 1 M 13 D 1 M 6 I 1 M 12 D 2 M 45 D 1 M 6
|
||||
vulgar: sacCer3_dna 491 162 - gi|330443489|ref|NC_001135.5| 23668 115569 + 267 M 29 29 5 0 2 I 0 8979 3 0 2 M 32 32 G 0 2 M 2 2 G 0 1 M 15 15 5 0 2 I 0 9551 3 0 2 M 3 3 G 1 0 M 5 5 G 0 2 M 3 3 G 0 1 M 4 4 G 0 1 M 18 18 S 1 1 5 0 2 I 0 55419 3 0 2 S 2 2 C 3 3 M 22 22 G 3 0 M 46 46 5 0 2 I 0 17594 3 0 2 M 14 14 G 0 1 M 9 9 G 1 0 M 15 15 G 0 3 M 17 17 G 0 3 M 1 1 G 0 1 M 13 13 G 0 1 M 6 6 G 1 0 M 12 12 G 0 2 M 45 45 G 0 1 M 6 6
|
||||
cigar: sacCer3_dna 529 78 - gi|330443667|ref|NC_001143.9| 641760 71883 - 267 M 31 I 3 M 4 I 2 M 19 D 3 M 9 D 1 M 6 I 1 M 7 D 154244 I 57 D 47 M 27 I 5 M 4 I 1 M 3 I 3 M 4 I 1 M 9 D 1 M 16 D 101116 I 31 M 25 D 1 M 15 I 1 M 9 I 1 M 2 I 1 M 14 M 20 D 177446 M 13 M 2 D 1 M 24 D 136697 I 7 D 6 I 1 D 1 I 1 D 1 I 1 D 1 I 1 D 1 I 2 D 1 I 1 D 1 I 1 D 1 I 3 D 1 I 2 D 1 I 1 D 1 I 1 D 1 I 2 D 2 I 2 D 2 I 17 M 14 I 2 M 22
|
||||
vulgar: sacCer3_dna 529 78 - gi|330443667|ref|NC_001143.9| 641760 71883 - 267 M 31 31 G 3 0 M 4 4 G 2 0 M 19 19 G 0 3 M 9 9 G 0 1 M 6 6 G 1 0 M 5 5 5 2 2 I 0 154244 I 57 0 I 0 47 3 2 2 M 25 25 G 5 0 M 4 4 G 1 0 M 3 3 G 3 0 M 4 4 G 1 0 M 9 9 G 0 1 M 14 14 5 2 2 I 0 101116 I 31 0 3 2 2 M 23 23 G 0 1 M 15 15 G 1 0 M 9 9 G 1 0 M 2 2 G 1 0 M 14 14 C 18 18 S 2 2 5 0 2 I 0 177442 3 0 2 S 1 1 C 12 12 M 2 2 G 0 1 M 22 22 5 2 2 I 0 136697 I 7 0 I 0 6 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 3 0 I 0 1 I 2 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 I 0 2 I 2 0 I 0 2 I 17 0 3 2 2 M 12 12 G 2 0 M 22 22
|
||||
-- completed exonerate analysis
|
||||
Reference in New Issue
Block a user